[AMBER] parmed gromber issues inappropriate disulfide warning based on CYS/MET approach

From: Chris Neale <candrewn.gmail.com>
Date: Fri, 3 Feb 2017 14:57:39 -0700

Dear developers:

When using the charmm36 forcefield implemented in gromacs, then using the
gromacs .top file to generate amber inputs using parmed/gromber from
ambertools 16, parmed will sometimes issue a warning about missing
disulfide bonds that it reposts as CYS-CYS distances, but are actually
CYS-MET distance.


MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
                  Angstroms. Rename CYS to CYX in the PDB file and use the
                  'bond' command in tleap to create the disulfide bond

### Usage:
parmed << EOF
gromber full.top $gmxgro topdir $topdir
outparm this.prmtop this.inpcrd

Obviously not a problem, just reporting.
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Received on Fri Feb 03 2017 - 14:00:03 PST
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